AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm?

From: Siddharth Rastogi <>
Date: Fri, 14 Nov 2008 06:02:34 -0800

Dear Amber users,

I want to rewrite topology file using rdparm. I have removed water using
stripwater command and edited topology file. But I need to remove the
counter metal ions also (say K+ ions). How to do this using rdparm?.
I have one more doubt. To calculate SASA ,whether I have to remove
crystallographic waters also from the protein?.

Thanks in advance,

Siddharth Rastogi

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Received on Fri Dec 05 2008 - 14:45:18 PST
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